[2024-01-24 12:44:42,335] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:42,339] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:42,339] [INFO] DQC Reference Directory: /var/lib/cwl/stg19aae36e-4d46-4bc8-95f3-8c4e4c163567/dqc_reference
[2024-01-24 12:44:43,683] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:43,684] [INFO] Task started: Prodigal
[2024-01-24 12:44:43,684] [INFO] Running command: gunzip -c /var/lib/cwl/stgeaad7cb0-b6f4-4d59-ac54-0c179fa5e805/GCF_012979235.1_ASM1297923v1_genomic.fna.gz | prodigal -d GCF_012979235.1_ASM1297923v1_genomic.fna/cds.fna -a GCF_012979235.1_ASM1297923v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:50,649] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:50,649] [INFO] Task started: HMMsearch
[2024-01-24 12:44:50,649] [INFO] Running command: hmmsearch --tblout GCF_012979235.1_ASM1297923v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg19aae36e-4d46-4bc8-95f3-8c4e4c163567/dqc_reference/reference_markers.hmm GCF_012979235.1_ASM1297923v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:50,910] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:50,911] [INFO] Found 6/6 markers.
[2024-01-24 12:44:50,936] [INFO] Query marker FASTA was written to GCF_012979235.1_ASM1297923v1_genomic.fna/markers.fasta
[2024-01-24 12:44:50,937] [INFO] Task started: Blastn
[2024-01-24 12:44:50,937] [INFO] Running command: blastn -query GCF_012979235.1_ASM1297923v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg19aae36e-4d46-4bc8-95f3-8c4e4c163567/dqc_reference/reference_markers.fasta -out GCF_012979235.1_ASM1297923v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:51,647] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:51,651] [INFO] Selected 18 target genomes.
[2024-01-24 12:44:51,652] [INFO] Target genome list was writen to GCF_012979235.1_ASM1297923v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:51,683] [INFO] Task started: fastANI
[2024-01-24 12:44:51,684] [INFO] Running command: fastANI --query /var/lib/cwl/stgeaad7cb0-b6f4-4d59-ac54-0c179fa5e805/GCF_012979235.1_ASM1297923v1_genomic.fna.gz --refList GCF_012979235.1_ASM1297923v1_genomic.fna/target_genomes.txt --output GCF_012979235.1_ASM1297923v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:03,400] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:03,400] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg19aae36e-4d46-4bc8-95f3-8c4e4c163567/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:03,400] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg19aae36e-4d46-4bc8-95f3-8c4e4c163567/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:03,414] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:45:03,414] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:03,414] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Dissulfurirhabdus thermomarina	strain=SH388	GCA_012979235.1	1765737	1765737	type	True	100.0	806	808	95	conclusive
Dissulfurirhabdus thermomarina	strain=DSM 100025	GCA_010499435.1	1765737	1765737	type	True	99.7768	668	808	95	conclusive
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	76.507	156	808	95	below_threshold
Desulfacinum hydrothermale	strain=DSM 13146	GCA_900176285.1	109258	109258	type	True	76.3904	58	808	95	below_threshold
Geobacter grbiciae	strain=DSM 13689	GCA_018531165.1	155042	155042	type	True	76.2857	76	808	95	below_threshold
Desulfuromonas versatilis	strain=NIT-T3	GCA_019704135.1	2802975	2802975	type	True	76.1012	89	808	95	below_threshold
Desulfarculus baarsii	strain=DSM 2075	GCA_000143965.1	453230	453230	type	True	76.0106	86	808	95	below_threshold
Geomonas anaerohicana	strain=Red421	GCA_016458305.1	2798583	2798583	type	True	75.9737	69	808	95	below_threshold
Geomonas limicola	strain=Red745	GCA_014193675.1	2740186	2740186	type	True	75.9483	79	808	95	below_threshold
Pseudodesulfovibrio indicus	strain=DSM 101483	GCA_004365595.1	1716143	1716143	type	True	75.8738	80	808	95	below_threshold
Pseudodesulfovibrio indicus	strain=J2	GCA_001563225.1	1716143	1716143	type	True	75.8718	80	808	95	below_threshold
Geomonas azotofigens	strain=Red51	GCA_018919395.1	2843196	2843196	type	True	75.7913	82	808	95	below_threshold
Deferrisoma camini	strain=S3R1	GCA_000526155.1	1035120	1035120	type	True	75.6384	164	808	95	below_threshold
Thiohalorhabdus denitrificans	strain=HL 19	GCA_001399755.1	381306	381306	type	True	75.6256	97	808	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	75.5457	108	808	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:03,416] [INFO] DFAST Taxonomy check result was written to GCF_012979235.1_ASM1297923v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:03,417] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:03,417] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:03,417] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg19aae36e-4d46-4bc8-95f3-8c4e4c163567/dqc_reference/checkm_data
[2024-01-24 12:45:03,418] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:03,446] [INFO] Task started: CheckM
[2024-01-24 12:45:03,446] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012979235.1_ASM1297923v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012979235.1_ASM1297923v1_genomic.fna/checkm_input GCF_012979235.1_ASM1297923v1_genomic.fna/checkm_result
[2024-01-24 12:45:29,610] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:29,611] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:29,636] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:29,637] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:29,637] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012979235.1_ASM1297923v1_genomic.fna/markers.fasta)
[2024-01-24 12:45:29,638] [INFO] Task started: Blastn
[2024-01-24 12:45:29,638] [INFO] Running command: blastn -query GCF_012979235.1_ASM1297923v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg19aae36e-4d46-4bc8-95f3-8c4e4c163567/dqc_reference/reference_markers_gtdb.fasta -out GCF_012979235.1_ASM1297923v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:30,726] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:30,731] [INFO] Selected 24 target genomes.
[2024-01-24 12:45:30,732] [INFO] Target genome list was writen to GCF_012979235.1_ASM1297923v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:30,805] [INFO] Task started: fastANI
[2024-01-24 12:45:30,806] [INFO] Running command: fastANI --query /var/lib/cwl/stgeaad7cb0-b6f4-4d59-ac54-0c179fa5e805/GCF_012979235.1_ASM1297923v1_genomic.fna.gz --refList GCF_012979235.1_ASM1297923v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012979235.1_ASM1297923v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:45:44,523] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:44,538] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:45:44,538] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_012979235.1	s__Dissulfurirhabdus thermomarina	100.0	806	808	d__Bacteria;p__Desulfobacterota;c__Dissulfuribacteria;o__Dissulfuribacterales;f__Dissulfurirhabdaceae;g__Dissulfurirhabdus	95.0	99.96	99.96	0.96	0.96	2	conclusive
GCA_002419025.1	s__UBA5754 sp002419025	76.9963	95	808	d__Bacteria;p__Desulfobacterota;c__Dissulfuribacteria;o__Dissulfuribacterales;f__UBA5754;g__UBA5754	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003751635.1	s__Inmirania thermothiophila	76.519	155	808	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-100275;f__DSM-100275;g__Inmirania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000143965.1	s__Desulfarculus baarsii	76.0461	84	808	d__Bacteria;p__Desulfobacterota;c__Desulfarculia;o__Desulfarculales;f__Desulfarculaceae;g__Desulfarculus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018902755.1	s__SURF-10 sp018902755	75.9995	114	808	d__Bacteria;p__Desulfobacterota;c__Desulfarculia;o__Desulfarculales;f__Desulfarculaceae;g__SURF-10	95.0	99.98	99.96	0.97	0.96	6	-
GCA_003605055.1	s__SURF-10 sp003605055	75.9524	115	808	d__Bacteria;p__Desulfobacterota;c__Desulfarculia;o__Desulfarculales;f__Desulfarculaceae;g__SURF-10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016874975.1	s__VGSQ01 sp016874975	75.9498	100	808	d__Bacteria;p__Desulfobacterota;c__Desulfobaccia;o__Desulfobaccales;f__0-14-0-80-60-11;g__VGSQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018623495.1	s__JAAZVP01 sp018623495	75.8768	68	808	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Halothiobacillales;f__JAAZVP01;g__JAAZVP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018819925.1	s__SURF-10 sp018819925	75.8062	92	808	d__Bacteria;p__Desulfobacterota;c__Desulfarculia;o__Desulfarculales;f__Desulfarculaceae;g__SURF-10	95.0	99.87	99.83	0.95	0.93	4	-
GCA_002432195.1	s__UBA5852 sp002432195	75.7271	100	808	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA5852;g__UBA5852	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012798435.1	s__JAAZNF01 sp012798435	75.7086	92	808	d__Bacteria;p__Myxococcota;c__B64-G9;o__B64-G9;f__B64-G9;g__JAAZNF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003242475.1	s__ZC4RG40 sp003242475	75.695	57	808	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Vulgatibacteraceae;g__ZC4RG40	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000526155.1	s__Deferrisoma camini	75.69	157	808	d__Bacteria;p__Desulfobacterota_C;c__Deferrisomatia;o__Deferrisomatales;f__Deferrisomataceae;g__Deferrisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016218705.1	s__JACRDC01 sp016218705	75.6546	138	808	d__Bacteria;p__Desulfobacterota;c__Desulfarculia;o__Desulfarculales;f__Desulfarculaceae;g__JACRDC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002347815.1	s__UBA2251 sp002347815	75.6366	58	808	d__Bacteria;p__Desulfobacterota;c__Syntrophia;o__Syntrophales;f__UBA2251;g__UBA2251	95.0	99.94	99.94	0.93	0.93	2	-
GCF_003337735.1	s__Thioalbus denitrificans	75.5457	108	808	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-26407;f__DSM-26407;g__Thioalbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016208645.1	s__2-02-FULL-66-22 sp016208645	75.4144	60	808	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Methylomirabilales;f__2-02-FULL-66-22;g__2-02-FULL-66-22	95.0	98.75	98.75	0.78	0.78	2	-
GCA_011523845.1	s__WTFV01 sp011523845	75.01	75	808	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__WTFV01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:45:44,540] [INFO] GTDB search result was written to GCF_012979235.1_ASM1297923v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:45:44,540] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:45:44,544] [INFO] DFAST_QC result json was written to GCF_012979235.1_ASM1297923v1_genomic.fna/dqc_result.json
[2024-01-24 12:45:44,544] [INFO] DFAST_QC completed!
[2024-01-24 12:45:44,544] [INFO] Total running time: 0h1m2s